A method of fabricating a contact hole structure includes providing a substrate with an epitaxial layer embedded therein. Next, an interlayer dielectric is formed to cover the substrate. After that, a first hole is formed in the interlayer dielectric and the epitaxial layer. Later, a mask layer is formed to cover a sidewall of the first hole and expose a bottom of the first hole. Subsequently, a second hole is formed by etching the epitaxial layer at the bottom of the first hole and taking the mask layer and the interlayer dielectric as a mask, wherein the first hole and the second hole form a contact hole. Then, the mask layer is removed. Finally, a silicide layer is formed to cover the contact hole.